NM_000546.6(TP53):c.79C>G (p.Pro27Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 17, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002423240.3

Allele description [Variation Report for NM_000546.6(TP53):c.79C>G (p.Pro27Ala)]

NM_000546.6(TP53):c.79C>G (p.Pro27Ala)

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.79C>G (p.Pro27Ala)

HGVS:

NC_000017.11:g.7676399G>C
NG_017013.2:g.16152C>G
NM_000546.6:c.79C>GMANE SELECT
NM_001126112.3:c.79C>G
NM_001126113.3:c.79C>G
NM_001126114.3:c.79C>G
NM_001126118.2:c.-39C>G
NM_001276695.3:c.-39C>G
NM_001276696.3:c.-39C>G
NM_001276760.3:c.-39C>G
NM_001276761.3:c.-39C>G
NP_000537.3:p.Pro27Ala
NP_001119584.1:p.Pro27Ala
NP_001119585.1:p.Pro27Ala
NP_001119586.1:p.Pro27Ala
LRG_321:g.16152C>G
NC_000017.10:g.7579717G>C
NM_000546.4:c.79C>G

Protein change:

P27A

Links:

dbSNP: rs922736614

NCBI 1000 Genomes Browser:

rs922736614

Molecular consequence:

NM_001126118.2:c.-39C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276695.3:c.-39C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276696.3:c.-39C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276760.3:c.-39C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276761.3:c.-39C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.79C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.79C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.79C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.79C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002679411	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 17, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12826609, 30224644 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002679411

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 17, 2024)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.

Kato S, Han SY, Liu W, Otsuka K, Shibata H, Kanamaru R, Ishioka C.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8424-9. Epub 2003 Jun 25.

PubMed [citation]

PMID:: 12826609
PMCID:: PMC166245

Mutational processes shape the landscape of TP53 mutations in human cancer.

Giacomelli AO, Yang X, Lintner RE, McFarland JM, Duby M, Kim J, Howard TP, Takeda DY, Ly SH, Kim E, Gannon HS, Hurhula B, Sharpe T, Goodale A, Fritchman B, Steelman S, Vazquez F, Tsherniak A, Aguirre AJ, Doench JG, Piccioni F, Roberts CWM, et al.

Nat Genet. 2018 Oct;50(10):1381-1387. doi: 10.1038/s41588-018-0204-y. Epub 2018 Sep 17.

PubMed [citation]

PMID:: 30224644
PMCID:: PMC6168352

Details of each submission

From Ambry Genetics, SCV002679411.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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